Is such a thing possible? Since usually the good gods of D&D are allied. (such as Helm, Tyr, Ilmater etc. from FR. Usually I thought it would be one side which mistakenly believes itself to be good but which is in fact evil.)
Quote from FR supplement Lords of Darkness on the Twisted Rune (pg. 177) "The Rune has even been known to hire good adventurers to further their plans, never revealing the ultimate source of their funds." This leads to an interesting scenario where a good man fights for an evil cause, finds out it is evil, and then seeks revenge for having been used once he discovers that the cause he has been fighting for is in fact not good but evil.
I guess it depends on what perspective or agency is declaring both groups to be good. Except in an alignment centric D&D universe, and of course in Cthulu, good and evil are almost always subjective. Did Darth Vader consider himself evil? Probably not. He probably just saw himself as using whatever tools necessary to bring order to the universe, a result he probably considered to be "Good". Throughout the history of mankind, I would imagine that almost every group ever involved in a conflict with another party, believed themselves to be good, to be right. So, not only can two forces be in conflict and both believe themselves to be good, I believe almost all do believe they are good.